From pault@rogan.reading.sgi.com Mon Jul 12 11:47:02 1993 From: pault@rogan.reading.sgi.com (Paul Townsend) Message-Id: <9307121047.ZM14962@rogan.reading.sgi.com> Date: Mon, 12 Jul 1993 10:47:02 +0100 To: chemistry@ccl.net Subject: platforms I do not wish to hijack this mail exploder for commercial purposes. I would however comment that a computer system is just that - a system. CPU performance is a very important component of that system, but so are the io and graphics systems. Benchmarks tend to measure CPU performance. This is very useful, but users ultimatley will want to run an application, not a 100x100 matrix multiplication. One of the greatest problems confronting designers is the rapid increase in the speed of the CPU compared with the disks and other io components. Hence the various caching techiniques used by most vendors. My personal belief is that an increasing amount of effort will be spent on improving data through-put. These problems are further compounded when multiple CPU's are involved. Fun isn't it ? Paul (a Silicon Graphics Employee). -- _________________________________________________________________________ Paul Townsend | Mail Stop - IUK-311 Sales Support | Fax - +44 (0)734 302550 Silicon Graphics | Tele - +44 (0)734 306222 Forum 1, Station Rd, Theale | Email - pault@reading.sgi.com Reading, RG7 4RA UK | V Mail # - 9265 _________________________________________________________________________ From s.green@ic.ac.uk Mon Jul 12 12:12:52 1993 From: s.green@ic.ac.uk Message-Id: <9307121108.AA18702@cscmgb.cc.ic.ac.uk> Subject: MOPAC sparkles To: CHEMISTRY@ccl.net Date: Mon, 12 Jul 93 12:08:05 bst Dear All, I've been using MOPAC sparkles to recreate local environmental effects in proteins and then predict the pka of histidine residues from the perturbed molecular electrostatic potential. The problem I have is that MOPAC is restricted to integer values of charge for its sparkles. I know this can be done in gaussian but I've found that any such charge scheme does not work with the semiempirical wavefunctions expressed in gaussian. Has anybody modified MOPAC such that fractional charges may be used? Many Thanks, Stuart --- Stuart Green sgreen@ic.ac.uk Molecular Modelling Laboratory Tel: 071-589-5111 (x3988) Department of Chemistry Imperial College London From markm@portal.vpharm.com Mon Jul 12 04:56:00 1993 From: markm@portal.vpharm.com (Mark Murcko) Message-Id: <9307121356.AA20420@portal.vpharm.com> Subject: Looking for QSAR studies on tricyclic antidepressants To: chemistry@ccl.net Date: Mon, 12 Jul 1993 09:56:00 -0500 (EDT) Hey gang, we're looking for a quick lead to some of the leading QSAR work done on the tricyclic antidepressants. It doesn't have to be the most recent work -- we are looking for papers that cover many compounds and use a variety of approache. As I'm sure most of the authors of these papers read this newsgroup, I thought I'd begin here...any pointers welcome! / Mark From carlos@penelope.bio.cornell.edu Mon Jul 12 06:08:24 1993 Date: Mon, 12 Jul 93 10:08:24 -0400 From: carlos@penelope.bio.cornell.edu (Carlos Faerman) Message-Id: <9307121408.AA11127@penelope.bio.cornell.edu> To: chemistry@ccl.net Subject: e-mail address of Dr. Angelo Vedani I would like to get Dr. Vedani's postal and e-mail addresses. I remember he used to work in USA, but he has now gone back to Europe. Incidentally, is his code "YETI" available? Thanks Carlos H. Faerman PS: you can send your replies directly to me. CHF From scsupham@reading.ac.uk Mon Jul 12 15:13:06 1993 From: scsupham@reading.ac.uk Date: Mon, 12 Jul 93 15:22:20 BST Message-Id: <11367.9307121422@scsscsc3> To: chemistry@ccl.net Subject: Simulating NMR spectra ---------- X-Sun-Data-Type: text X-Sun-Data-Description: text X-Sun-Data-Name: text X-Sun-Content-Lines: 12 Dear All, I'd like to simulate the 13C and 1H spectra for some TM complexes. Does anyone have any code (free or otherwise) to do this please ? best wishes, john upham John Upham, Dept. of Chemistry, University of Reading, Berks., RG6 2AD, UK. Email: scsupham%reading.ac.uk@uk.ac (BITnet), scsupham@uk.ac.reading (Janet) Voice: +44 734 875123 x7441 (day), Fax: +44 734 311610 ---------- X-Sun-Data-Type: default X-Sun-Data-Description: default X-Sun-Data-Name: .signature X-Sun-Content-Lines: 3 John Upham, Dept. of Chemistry, University of Reading, Berks., RG6 2AD, UK. Email: scsupham%reading.ac.uk@uk.ac (BITnet), scsupham@uk.ac.reading (Janet) Voice: +44 734 875123 x7441 (day), Fax: +44 734 311610 From adit@Kodak.COM Mon Jul 12 06:56:13 1993 Date: Mon, 12 Jul 93 10:56:13 EDT From: adit@Kodak.COM (Adi Treasurywala) Message-Id: <9307121456.AA25965@bcc9.kodak.com> To: chemistry@ccl.net Subject: Programs that dock inhibitors. Folks, We are putting together a paper that describes a "new" docking method and I was hoping to include in it a table that cited the known published methods ( no unpublished refs please). The table would have several columns as shown below. Any and all contributions of your favourite method would be most welcome at this stage. I would appreciate hearing from you before the weekend if at all possible. TABLE: Reference | 6 Degrees of freedom | Allowed Flexibility | Allowed Flexibility | for the guest? | for the Guest | for the Host ------------------------------------------------------------------------------- | (Y/N) | Tors only | ALL | Tors only | ALL | | | | | Thanks in advance for your help. Adi M Treasurywala,Sterling Winthrop Inc,1250 South Collegeville Road, PO Box 5000, Collegeville, PA 19426-0900,Voice (215)983-6610 FAX (215)983-5559, INTERNET adit@kodak.com PS: If this works well I would like to include an acknowledgement to the net. Any advice on the appropriateness or format of that?(Jan? Doug? Others?...) From WONG@spacvax.rice.edu Mon Jul 12 06:07:09 1993 Date: Mon, 12 Jul 1993 11:07:09 -0500 (CDT) From: WONG@spacvax.rice.edu To: chemistry@ccl.net Message-Id: <930712110710.2020006a@spacvax.rice.edu> Subject: need your help Dear friends, I am looking for some references about how the shape of atoms will affect the parameters a,b of the van der Waals' equation. Could somebody recommend some appropriate papers, journals or books for me to read? My E-mail address is: wong@spacvax.rice.edu Thank You in advance! Yours Sincerely, Abby Wong From ssidner@karplus.unmc.edu Mon Jul 12 06:08:34 1993 Date: Mon, 12 Jul 93 11:08:34 CDT From: ssidner@karplus.unmc.edu (Steve Sidner) Message-Id: <9307121608.AA08489@karplus.unmc.edu> To: chemistry@ccl.net Subject: Re: which brand of workstation? Peter Shenkin wrote: > OpenGL would also allow the many skilled graphics programmers out there > who have come to know and love GL to apply their skills in a manner that > will make newly written programs run well across a wide variety of > architectures. But OpenGL is in its infancy, and "time will tell" > whether it will pan out. Yes, Peter, but how much time?! I agree with your analysis about SGI completely. Over the past 5 years, we gave up on other platforms, because the longterm software support just wasn't there. Fortunately, the SGI is a good machine. But not necessarily the best, for our applications. I'd love to see OpenGL. I'll bet other companies could build as good an implementations as SGI, especially Evans & Sutherland. But I've been hearing about OpenGL for so long (three years) that I've given up on it. Heck, it's basically just a spec. GL works now on SGI, it works over a network, between two SGIs. So what's the big deal?! Market share. PEX was supposed to be the "OpenGL" of this decade. But performance, functionality, and lack of SGI support is killing it. In fact the last time I heard about OpenGL was when SGI trotted it out to qwell a flurry of interest in PEX. SGI simply has a good deal and doesn't want to screw it up. Steve Sidner Eppley Institute, University of Nebraska Medical Center 600 S. 42nd St., Omaha, NE, 68198-6805, U.S.A. (402) 559-4921, FAX: (402) 559-4651 ssidner@unmc.edu ssidner@unmcvm.bitnet From CHEM8@VAXA.YORK.AC.UK Mon Jul 12 19:07:33 1993 Message-Id: <199307121855.AA04432@oscsunb.ccl.net> Date: Mon, 12 Jul 93 19:57 BST From: "John Waite, Tel 1-7238958, N.H.R.F., Vas. Konstantinou 48, Athens 116-35" To: CHEMISTRY Subject: Contact for Prof. R.M.Stevens Could anyone let me know the whereabouts of Professor R.M.Stevens - the Theoretical Chemist who dealt mainly with STOs? Thank you, John From NEELY@DUCVAX.AUBURN.EDU Mon Jul 12 08:25:00 1993 Date: Mon, 12 Jul 1993 14:25 CST From: NEELY@DUCVAX.AUBURN.EDU Subject: AMBER 4.0/CARNAL To: chemistry@ccl.net Message-Id: <01H0GI7JQLK0000LHH@DUCVAX.AUBURN.EDU> I'd appreciate it if someone could e-mail me a copy of an input file for CARNAL (the new analysis program for AMBER 4.0), which has been successfully used to extract PDB-format coordinate data >from the output of an MD run. The instructions *seem* straight- forward enough, but I haven't been able to get it to work. Thanks a lot! Irene Newhouse From dchin%emperor@harvard.harvard.edu Mon Jul 12 14:50:44 1993 Date: Mon, 12 Jul 93 18:50:44 -0400 From: dchin%emperor@harvard.harvard.edu (Donovan Chin) Message-Id: <9307122250.AA15652@emperor.harvard.edu> To: chemistry@ccl.net Subject: THE CHARMM-BBS Dear Netters; There exists a bulletin board service (bbs) for users of the CHARMM (Chemistry at HARvard Macromolecular Mechanics) modeling software. This bbs has been dedicated to applications of CHARMM and the science behind it. --> This service is available to anyone who uses CHARMM(m). <-- --> It is designed so that users can share CHARMM information, <-- --> or scripts, with others quickly and efficiently via e-mail. <-- ----- --> There are over 150 subscribers in the US, Europe, Scandinavia <-- --> and Asia. Several subscriptions are links to other charmm <-- --> groups at universities, industrial or government groups. <-- +++++++++++++++++++++++++++++++++++++++++++++++++++++++++ + + + REQUESTS TO JOIN, or information, can be sent to: + + charmm-bbs-request@emperor.harvard.edu + + + +++++++++++++++++++++++++++++++++++++++++++++++++++++++++ ----------------- {After subscribing}: Any charmm related questions/comments or scripts you would like to share, are simply posted to the bbs in the form of e-mail. All subscribers will receive all e-mail that is sent to the bbs. There is a message log that keeps a list of all postings. ***>> DISCLAIMER <<*** The charmm-bbs is an informal and secular service that has proved successful from its initial conception (1 year). It is not maintained by anyone who develops and/or markets CHARMM(m). It is therefore NOT AFFILIATED WITH MSI OR ANY ACADEMIC GROUPS. However, many members of the CHARMM development and MSI community do participate. The charmm-bbs was designed for charmm users by charmm users.. Regards, Donovan Chin charmm-bbs-administrator ------------------------------------------------------------------- DONOVAN CHIN Harvard University E-mail: dchin@emperor.harvard.edu Department of Chemistry Phone: (617) 495-9435 12 Oxford St. Fax: (617) 495-9857 Cambridge, MA 02138, USA ------------------------------------------------------------------- From jle@world.std.com Mon Jul 12 15:22:03 1993 Date: Mon, 12 Jul 1993 19:22:03 -0400 From: jle@world.std.com (Joe M Leonard) Message-Id: <199307122322.AA19844@world.std.com> To: chemistry@ccl.net Subject: Seeking information on date/time fns in IBM XLF... Is there a counterpart to the fgets() routine on the SGI which returns a date/time stamp of the form 12 Jul 1993 16:25:42 or something like that? I tried to read the Info pages on intrinsic functions, but the bloody things exits when I select that entry in the XLF manual "book"... Any comments would be appreciated - even separate functions callable >from Fortran that provide date-string and time-string (I can append, etc.) Thanx in advance! Joe Leonard jle@world.std.com From jkl@ccl.net Mon Jul 12 15:39:37 1993 From: Jan Labanowski Date: Mon, 12 Jul 1993 19:39:37 -0400 Message-Id: <199307122339.AA06584@krakow.ccl.net> To: chemistry@ccl.net Subject: Will be away but list stays Dear Ccmputational Chemists in a Cyberspace, I will be gone for over 5 weeks starting this Friday, part of which might be vacations (I hope --- tips on where to stay in Vienna and Piwniczna Zdroj on a scientist's budget but not among cockroaches {(:-0} are welcome). I decided to leave the list in good hands of Rob Berry (primarily), and Dave Heisterberg (when his busy schedule allows --- he will be now working for both of us). They will be sending e-mail from my address, but it will not be me. Please understand that some issues may have to wait till I return, and I will be incomunicado all this time. Recently, few of our subscribers broke the rules of the list with their address inquires. Please keep the noise down... The full set of rules of this list is available from anonymous ftp on www.ccl.net: ftp www.ccl.net Login: anonymous Password: Your_email_address cd /pub/chemistry get help quit The help file is also available via e-mail. Send the message: send help from chemistry to OSCPOST@ccl.net or OSCPOST@OHSTPY.BITNET. Here are the main do's and don'ts for the list. Examples of topics for the list are: - reports on bugs in chemistry software and possible work- arounds - new chemistry software announcements - announcements of computational chemistry-related workshops and symposia - new methods and techniques in computational chemistry - questions and answers about solving computational chemistry problems - programs and utilities - information on the availability of particular software, data, etc. - hardware-related issues relevant to the computational chemistry community - opinions about services and products Examples of topics which SHOULD NOT appear on this list are: - personal attacks - topics unrelated to computational chemistry - announcements of "vaporware" - annoucements of job openings or CV's. These are handled off line (see point V for more information). - address inquiries (you can post address inquiry only when you exhausted all other ways (i.e., looking up ACS Directory of Chemistry Departments in your library, contacting list coordinator, contacting the Postmaster at the target machine) Rules for commercial software announcements are described later in this file. III. HOW TO POST TO THE COMPUTATIONAL CHEMISTRY LIST. The list is uncensored, i.e. nobody screens the messages before they are posted. The machine delivers them automatically. Before you post to the list, be sure that your message is correct (use editor!) and adheres to the rules. Use lines shorter than 80 characters since many mailers truncate longer lines. Remember that what you post will be received by about 2000 people in many countries. However, do not feel overly paralyzed about this. Communication is a two-way street. Be concise though. Not everybody has superworkstations connected to a high-speed network. However, do not be overly concise. If you have a question to the list, describe your problem, and why you need it --- try to educate and be educated. Also, summarize to the list the responses you got. We want to know what you know. Jan jkl@ccl.net -- Dr. Jan K. Labanowski, Senior Research/Supercomputer Scientist/Specialist, etc. Ohio Supercomputer Center, 1224 Kinnear Rd, Columbus, OH 43212-1163 ph:(614)-292-9279, FAX:(614)-292-7168, E-mail: jkl@ccl.net JKL@OHSTPY.BITNET From raman@bioc01.uthscsa.edu Mon Jul 12 15:09:08 1993 From: raman@bioc01.uthscsa.edu (C.S.RAMAN) Message-Id: <9307130109.AA08352@bioc01.uthscsa.edu> Subject: Fullerenes! To: chemistry@ccl.net Date: Mon, 12 Jul 1993 20:09:08 -0500 (CDT) Dear Netters I just received the following information regarding the availability of commercial fullerenes. Anyone interested can contact the parties listed below! :) A NEW SOURCE OF FULLERENES FROM LATVIA ============================================================================= Prof. Robert M. Metzger (U. Alabama) visited Riga, Latvia in June 1993. A Riga group can supply fullerenes in high purity at low cost. 1) 99.9% purity C60 at U.S.$ 310 per gram 2) fullerene mixture c60:c70:Cx=73%:24%:3% 3) joint ventures for obtaining, selling, and investigation of fullerenes are possible. Contact: Dr. S. Alexandrow and Dr. Y. Kalnach Institute of Physical Energetics, Latvian Academy of Sciences Aizkraukles street 21, LV-1006 Riga, Latvia, voice 371-2-558-621, fax 371-2-551-394 ============================================================================ -- C.S.Raman raman@bioc01.uthscsa.edu - Internet UNIX Programming & Administration 70412.2354@compuserve.com - CIS SPARC & SGI Systems raman@hermes.chpc.utexas.edu - CHPC Department of Biochemistry craman@launchpad.unc.edu UTHSCSA 7703 Floyd Curl Dr. (210) 567-6623 [Tel] San Antonio, TX 78284-7760 (210) 567-6595 [Fax] ****************************************************************************** If a man's wit be wandering, let him study the Mathematics -Francis Bacon ******************************************************************************